Starting phenix.real_space_refine on Tue Jun 25 11:08:25 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8y3x_38906/06_2024/8y3x_38906_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8y3x_38906/06_2024/8y3x_38906.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.11 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8y3x_38906/06_2024/8y3x_38906.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8y3x_38906/06_2024/8y3x_38906.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8y3x_38906/06_2024/8y3x_38906_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8y3x_38906/06_2024/8y3x_38906_updated.pdb" } resolution = 3.11 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.012 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 6 5.49 5 S 30 5.16 5 C 4907 2.51 5 N 1409 2.21 5 O 1405 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C TYR 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 302": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/chem_data/mon_lib" Total number of atoms: 7757 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 1669 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1669 Classifications: {'peptide': 218} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 7, 'TRANS': 210} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "B" Number of atoms: 1670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1670 Classifications: {'peptide': 218} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 7, 'TRANS': 210} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "C" Number of atoms: 1918 Number of conformers: 1 Conformer: "" Number of residues, atoms: 299, 1918 Classifications: {'peptide': 299} Incomplete info: {'truncation_to_alanine': 108} Link IDs: {'PTRANS': 9, 'TRANS': 289} Unresolved non-hydrogen bonds: 393 Unresolved non-hydrogen angles: 505 Unresolved non-hydrogen dihedrals: 313 Unresolved non-hydrogen chiralities: 35 Planarities with less than four sites: {'GLN:plan1': 10, 'TYR:plan': 4, 'ASN:plan1': 6, 'TRP:plan': 2, 'ASP:plan': 14, 'PHE:plan': 3, 'GLU:plan': 11, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 248 Chain: "D" Number of atoms: 1888 Number of conformers: 1 Conformer: "" Number of residues, atoms: 299, 1888 Classifications: {'peptide': 299} Incomplete info: {'truncation_to_alanine': 117} Link IDs: {'PTRANS': 9, 'TRANS': 289} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 425 Unresolved non-hydrogen angles: 547 Unresolved non-hydrogen dihedrals: 337 Unresolved non-hydrogen chiralities: 41 Planarities with less than four sites: {'GLN:plan1': 13, 'TYR:plan': 3, 'ASN:plan1': 6, 'TRP:plan': 2, 'ASP:plan': 12, 'PHE:plan': 5, 'GLU:plan': 11, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 264 Chain: "E" Number of atoms: 550 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 550 Classifications: {'peptide': 111} Incomplete info: {'truncation_to_alanine': 93} Link IDs: {'TRANS': 110} Unresolved non-hydrogen bonds: 350 Unresolved non-hydrogen angles: 437 Unresolved non-hydrogen dihedrals: 275 Unresolved non-hydrogen chiralities: 25 Planarities with less than four sites: {'GLN:plan1': 20, 'HIS:plan': 1, 'TYR:plan': 2, 'ASN:plan1': 5, 'ASP:plan': 2, 'PHE:plan': 2, 'GLU:plan': 14, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 233 Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 8.11, per 1000 atoms: 1.05 Number of scatterers: 7757 At special positions: 0 Unit cell: (68.04, 78.96, 197.4, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 30 16.00 P 6 15.00 O 1405 8.00 N 1409 7.00 C 4907 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.51 Conformation dependent library (CDL) restraints added in 2.1 seconds 2270 Ramachandran restraints generated. 1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2100 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 43 helices and 7 sheets defined 56.4% alpha, 5.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.97 Creating SS restraints... Processing helix chain 'A' and resid 41 through 49 Processing helix chain 'A' and resid 74 through 79 Processing helix chain 'A' and resid 96 through 107 Proline residue: A 103 - end of helix Processing helix chain 'A' and resid 111 through 124 Processing helix chain 'A' and resid 128 through 130 No H-bonds generated for 'chain 'A' and resid 128 through 130' Processing helix chain 'A' and resid 135 through 137 No H-bonds generated for 'chain 'A' and resid 135 through 137' Processing helix chain 'A' and resid 140 through 154 removed outlier: 4.815A pdb=" N ASN A 154 " --> pdb=" O ARG A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 186 removed outlier: 4.436A pdb=" N VAL A 186 " --> pdb=" O GLU A 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 197 through 200 No H-bonds generated for 'chain 'A' and resid 197 through 200' Processing helix chain 'B' and resid 41 through 49 Processing helix chain 'B' and resid 74 through 77 No H-bonds generated for 'chain 'B' and resid 74 through 77' Processing helix chain 'B' and resid 96 through 107 Proline residue: B 103 - end of helix Processing helix chain 'B' and resid 111 through 123 Processing helix chain 'B' and resid 128 through 130 No H-bonds generated for 'chain 'B' and resid 128 through 130' Processing helix chain 'B' and resid 135 through 137 No H-bonds generated for 'chain 'B' and resid 135 through 137' Processing helix chain 'B' and resid 140 through 154 removed outlier: 5.012A pdb=" N ASN B 154 " --> pdb=" O ARG B 150 " (cutoff:3.500A) Processing helix chain 'B' and resid 170 through 186 removed outlier: 4.166A pdb=" N VAL B 186 " --> pdb=" O GLU B 182 " (cutoff:3.500A) Processing helix chain 'B' and resid 198 through 201 No H-bonds generated for 'chain 'B' and resid 198 through 201' Processing helix chain 'C' and resid 64 through 78 Processing helix chain 'C' and resid 81 through 106 removed outlier: 3.635A pdb=" N VAL C 90 " --> pdb=" O LEU C 86 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N LEU C 97 " --> pdb=" O ILE C 93 " (cutoff:3.500A) Proline residue: C 98 - end of helix removed outlier: 4.186A pdb=" N MET C 103 " --> pdb=" O SER C 99 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N VAL C 104 " --> pdb=" O VAL C 100 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N TYR C 105 " --> pdb=" O CYS C 101 " (cutoff:3.500A) Processing helix chain 'C' and resid 108 through 111 No H-bonds generated for 'chain 'C' and resid 108 through 111' Processing helix chain 'C' and resid 131 through 140 removed outlier: 3.887A pdb=" N ALA C 135 " --> pdb=" O ASP C 131 " (cutoff:3.500A) Processing helix chain 'C' and resid 155 through 164 removed outlier: 4.489A pdb=" N GLY C 160 " --> pdb=" O ASP C 157 " (cutoff:3.500A) removed outlier: 5.468A pdb=" N GLU C 161 " --> pdb=" O ALA C 158 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N PHE C 162 " --> pdb=" O LEU C 159 " (cutoff:3.500A) Processing helix chain 'C' and resid 190 through 193 No H-bonds generated for 'chain 'C' and resid 190 through 193' Processing helix chain 'C' and resid 195 through 206 removed outlier: 3.632A pdb=" N THR C 200 " --> pdb=" O GLU C 196 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N LEU C 201 " --> pdb=" O SER C 197 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ASP C 203 " --> pdb=" O ASN C 199 " (cutoff:3.500A) Processing helix chain 'C' and resid 222 through 224 No H-bonds generated for 'chain 'C' and resid 222 through 224' Processing helix chain 'C' and resid 230 through 269 removed outlier: 3.680A pdb=" N SER C 235 " --> pdb=" O VAL C 231 " (cutoff:3.500A) removed outlier: 4.899A pdb=" N ALA C 236 " --> pdb=" O GLY C 232 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N PHE C 247 " --> pdb=" O VAL C 243 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ARG C 261 " --> pdb=" O SER C 257 " (cutoff:3.500A) removed outlier: 5.657A pdb=" N ASP C 263 " --> pdb=" O PHE C 259 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N SER C 264 " --> pdb=" O ALA C 260 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ILE C 265 " --> pdb=" O ARG C 261 " (cutoff:3.500A) Processing helix chain 'C' and resid 277 through 299 Proline residue: C 281 - end of helix removed outlier: 3.511A pdb=" N GLY C 285 " --> pdb=" O PRO C 281 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N LEU C 289 " --> pdb=" O GLY C 285 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LEU C 296 " --> pdb=" O SER C 292 " (cutoff:3.500A) Processing helix chain 'C' and resid 303 through 319 removed outlier: 3.925A pdb=" N SER C 310 " --> pdb=" O LEU C 306 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N ALA C 311 " --> pdb=" O ARG C 307 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N GLN C 317 " --> pdb=" O ALA C 313 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N VAL C 318 " --> pdb=" O GLU C 314 " (cutoff:3.500A) Processing helix chain 'C' and resid 330 through 356 removed outlier: 4.134A pdb=" N LEU C 335 " --> pdb=" O ASP C 331 " (cutoff:3.500A) Processing helix chain 'D' and resid 64 through 78 Processing helix chain 'D' and resid 81 through 115 removed outlier: 4.159A pdb=" N LEU D 97 " --> pdb=" O ILE D 93 " (cutoff:3.500A) Proline residue: D 98 - end of helix Processing helix chain 'D' and resid 131 through 140 Processing helix chain 'D' and resid 155 through 163 removed outlier: 4.451A pdb=" N GLY D 160 " --> pdb=" O ASP D 157 " (cutoff:3.500A) removed outlier: 5.386A pdb=" N GLU D 161 " --> pdb=" O ALA D 158 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N PHE D 162 " --> pdb=" O LEU D 159 " (cutoff:3.500A) Processing helix chain 'D' and resid 190 through 193 No H-bonds generated for 'chain 'D' and resid 190 through 193' Processing helix chain 'D' and resid 195 through 206 removed outlier: 5.036A pdb=" N THR D 200 " --> pdb=" O GLU D 196 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N LEU D 201 " --> pdb=" O SER D 197 " (cutoff:3.500A) Processing helix chain 'D' and resid 220 through 263 removed outlier: 4.306A pdb=" N SER D 235 " --> pdb=" O VAL D 231 " (cutoff:3.500A) removed outlier: 5.143A pdb=" N ASP D 263 " --> pdb=" O PHE D 259 " (cutoff:3.500A) Processing helix chain 'D' and resid 265 through 270 Processing helix chain 'D' and resid 275 through 318 removed outlier: 3.512A pdb=" N ARG D 280 " --> pdb=" O GLY D 276 " (cutoff:3.500A) Proline residue: D 281 - end of helix removed outlier: 3.789A pdb=" N LEU D 289 " --> pdb=" O GLY D 285 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N SER D 310 " --> pdb=" O LEU D 306 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N ALA D 311 " --> pdb=" O ARG D 307 " (cutoff:3.500A) removed outlier: 4.726A pdb=" N VAL D 312 " --> pdb=" O LEU D 308 " (cutoff:3.500A) Processing helix chain 'D' and resid 330 through 358 removed outlier: 3.548A pdb=" N ARG D 357 " --> pdb=" O VAL D 353 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N HIS D 358 " --> pdb=" O GLN D 354 " (cutoff:3.500A) Processing helix chain 'E' and resid 81 through 122 Processing helix chain 'E' and resid 145 through 149 Processing helix chain 'E' and resid 153 through 189 Processing sheet with id= A, first strand: chain 'A' and resid 23 through 25 Processing sheet with id= B, first strand: chain 'A' and resid 206 through 210 Processing sheet with id= C, first strand: chain 'A' and resid 9 through 11 removed outlier: 6.729A pdb=" N TYR A 11 " --> pdb=" O GLN A 16 " (cutoff:3.500A) removed outlier: 5.658A pdb=" N GLN A 16 " --> pdb=" O TYR A 11 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 23 through 25 Processing sheet with id= E, first strand: chain 'B' and resid 31 through 35 removed outlier: 6.749A pdb=" N ARG B 206 " --> pdb=" O PHE B 32 " (cutoff:3.500A) removed outlier: 7.555A pdb=" N THR B 34 " --> pdb=" O ARG B 206 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N LEU B 208 " --> pdb=" O THR B 34 " (cutoff:3.500A) No H-bonds generated for sheet with id= E Processing sheet with id= F, first strand: chain 'B' and resid 81 through 84 removed outlier: 6.584A pdb=" N VAL B 158 " --> pdb=" O GLY B 82 " (cutoff:3.500A) removed outlier: 7.971A pdb=" N ILE B 84 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N LEU B 160 " --> pdb=" O ILE B 84 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N THR B 189 " --> pdb=" O LEU B 159 " (cutoff:3.500A) removed outlier: 7.835A pdb=" N ALA B 161 " --> pdb=" O THR B 189 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N LEU B 191 " --> pdb=" O ALA B 161 " (cutoff:3.500A) No H-bonds generated for sheet with id= F Processing sheet with id= G, first strand: chain 'B' and resid 9 through 11 removed outlier: 6.929A pdb=" N TYR B 11 " --> pdb=" O GLN B 16 " (cutoff:3.500A) removed outlier: 5.938A pdb=" N GLN B 16 " --> pdb=" O TYR B 11 " (cutoff:3.500A) 452 hydrogen bonds defined for protein. 1308 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.98 Time building geometry restraints manager: 3.87 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 2396 1.33 - 1.45: 1039 1.45 - 1.57: 4383 1.57 - 1.69: 10 1.69 - 1.81: 52 Bond restraints: 7880 Sorted by residual: bond pdb=" N VAL C 185 " pdb=" CA VAL C 185 " ideal model delta sigma weight residual 1.456 1.493 -0.037 1.19e-02 7.06e+03 9.58e+00 bond pdb=" N VAL C 186 " pdb=" CA VAL C 186 " ideal model delta sigma weight residual 1.456 1.493 -0.037 1.23e-02 6.61e+03 9.06e+00 bond pdb=" N VAL C 183 " pdb=" CA VAL C 183 " ideal model delta sigma weight residual 1.459 1.496 -0.037 1.25e-02 6.40e+03 8.72e+00 bond pdb=" N ILE C 121 " pdb=" CA ILE C 121 " ideal model delta sigma weight residual 1.459 1.494 -0.035 1.25e-02 6.40e+03 8.02e+00 bond pdb=" N ILE C 211 " pdb=" CA ILE C 211 " ideal model delta sigma weight residual 1.459 1.494 -0.035 1.25e-02 6.40e+03 7.96e+00 ... (remaining 7875 not shown) Histogram of bond angle deviations from ideal: 99.10 - 106.08: 155 106.08 - 113.06: 4410 113.06 - 120.04: 2646 120.04 - 127.03: 3478 127.03 - 134.01: 77 Bond angle restraints: 10766 Sorted by residual: angle pdb=" PB ATP B 301 " pdb=" O3B ATP B 301 " pdb=" PG ATP B 301 " ideal model delta sigma weight residual 139.87 129.08 10.79 1.00e+00 1.00e+00 1.16e+02 angle pdb=" PB ATP A 301 " pdb=" O3B ATP A 301 " pdb=" PG ATP A 301 " ideal model delta sigma weight residual 139.87 130.49 9.38 1.00e+00 1.00e+00 8.80e+01 angle pdb=" N ALA C 225 " pdb=" CA ALA C 225 " pdb=" C ALA C 225 " ideal model delta sigma weight residual 114.62 108.03 6.59 1.14e+00 7.69e-01 3.34e+01 angle pdb=" PA ATP B 301 " pdb=" O3A ATP B 301 " pdb=" PB ATP B 301 " ideal model delta sigma weight residual 136.83 131.79 5.04 1.00e+00 1.00e+00 2.54e+01 angle pdb=" N VAL C 100 " pdb=" CA VAL C 100 " pdb=" C VAL C 100 " ideal model delta sigma weight residual 112.96 108.55 4.41 1.00e+00 1.00e+00 1.95e+01 ... (remaining 10761 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.99: 4087 16.99 - 33.98: 378 33.98 - 50.97: 158 50.97 - 67.95: 37 67.95 - 84.94: 8 Dihedral angle restraints: 4668 sinusoidal: 1413 harmonic: 3255 Sorted by residual: dihedral pdb=" CA GLU E 114 " pdb=" C GLU E 114 " pdb=" N ARG E 115 " pdb=" CA ARG E 115 " ideal model delta harmonic sigma weight residual 180.00 153.16 26.84 0 5.00e+00 4.00e-02 2.88e+01 dihedral pdb=" CA HIS A 195 " pdb=" C HIS A 195 " pdb=" N ASP A 196 " pdb=" CA ASP A 196 " ideal model delta harmonic sigma weight residual 180.00 157.77 22.23 0 5.00e+00 4.00e-02 1.98e+01 dihedral pdb=" CA SER D 264 " pdb=" C SER D 264 " pdb=" N ILE D 265 " pdb=" CA ILE D 265 " ideal model delta harmonic sigma weight residual 180.00 157.84 22.16 0 5.00e+00 4.00e-02 1.96e+01 ... (remaining 4665 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.066: 1129 0.066 - 0.131: 153 0.131 - 0.197: 28 0.197 - 0.262: 4 0.262 - 0.328: 2 Chirality restraints: 1316 Sorted by residual: chirality pdb=" CB THR C 360 " pdb=" CA THR C 360 " pdb=" OG1 THR C 360 " pdb=" CG2 THR C 360 " both_signs ideal model delta sigma weight residual False 2.55 2.22 0.33 2.00e-01 2.50e+01 2.69e+00 chirality pdb=" CB VAL B 96 " pdb=" CA VAL B 96 " pdb=" CG1 VAL B 96 " pdb=" CG2 VAL B 96 " both_signs ideal model delta sigma weight residual False -2.63 -2.36 -0.26 2.00e-01 2.50e+01 1.75e+00 chirality pdb=" CA LEU C 198 " pdb=" N LEU C 198 " pdb=" C LEU C 198 " pdb=" CB LEU C 198 " both_signs ideal model delta sigma weight residual False 2.51 2.73 -0.22 2.00e-01 2.50e+01 1.22e+00 ... (remaining 1313 not shown) Planarity restraints: 1396 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS E 110 " 0.022 2.00e-02 2.50e+03 4.44e-02 1.97e+01 pdb=" C LYS E 110 " -0.077 2.00e-02 2.50e+03 pdb=" O LYS E 110 " 0.028 2.00e-02 2.50e+03 pdb=" N ALA E 111 " 0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ARG D 280 " 0.060 5.00e-02 4.00e+02 9.00e-02 1.29e+01 pdb=" N PRO D 281 " -0.156 5.00e-02 4.00e+02 pdb=" CA PRO D 281 " 0.046 5.00e-02 4.00e+02 pdb=" CD PRO D 281 " 0.050 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ALA E 104 " -0.015 2.00e-02 2.50e+03 2.97e-02 8.84e+00 pdb=" C ALA E 104 " 0.051 2.00e-02 2.50e+03 pdb=" O ALA E 104 " -0.019 2.00e-02 2.50e+03 pdb=" N LYS E 105 " -0.017 2.00e-02 2.50e+03 ... (remaining 1393 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.64: 105 2.64 - 3.21: 7305 3.21 - 3.77: 11814 3.77 - 4.34: 15243 4.34 - 4.90: 25530 Nonbonded interactions: 59997 Sorted by model distance: nonbonded pdb=" OG SER A 139 " pdb=" OE1 GLU A 142 " model vdw 2.075 2.440 nonbonded pdb=" O ASP A 169 " pdb=" OG SER A 173 " model vdw 2.117 2.440 nonbonded pdb=" NH2 ARG A 79 " pdb=" O GLY D 272 " model vdw 2.215 2.520 nonbonded pdb=" O ASP C 76 " pdb=" OG SER C 79 " model vdw 2.225 2.440 nonbonded pdb=" OH TYR B 11 " pdb=" OG1 THR B 43 " model vdw 2.244 2.440 ... (remaining 59992 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 11 or (resid 12 and (name N or name CA or name C \ or name O or name CB )) or resid 13 through 196 or (resid 197 through 198 and ( \ name N or name CA or name C or name O or name CB )) or resid 199 through 218 or \ resid 301)) selection = (chain 'B' and (resid 1 through 67 or (resid 68 and (name N or name CA or name C \ or name O or name CB )) or resid 69 or (resid 70 and (name N or name CA or name \ C or name O or name CB )) or resid 71 through 218 or resid 301)) } ncs_group { reference = (chain 'C' and ((resid 63 through 65 and (name N or name CA or name C or name O \ or name CB )) or resid 66 through 74 or (resid 75 through 76 and (name N or name \ CA or name C or name O or name CB )) or resid 77 through 220 or (resid 221 thro \ ugh 223 and (name N or name CA or name C or name O or name CB )) or resid 224 th \ rough 226 or (resid 227 and (name N or name CA or name C or name O or name CB )) \ or resid 228 through 229 or (resid 230 through 231 and (name N or name CA or na \ me C or name O or name CB )) or resid 232 or (resid 233 through 234 and (name N \ or name CA or name C or name O or name CB )) or resid 235 through 307 or (resid \ 308 through 319 and (name N or name CA or name C or name O or name CB )) or (res \ id 320 through 326 and (name N or name CA or name C or name O or name CB )) or r \ esid 327 through 331 or (resid 332 and (name N or name CA or name C or name O or \ name CB )) or resid 333 through 353 or (resid 354 and (name N or name CA or nam \ e C or name O or name CB )) or resid 355 through 359 or (resid 360 through 361 a \ nd (name N or name CA or name C or name O or name CB )))) selection = (chain 'D' and (resid 63 through 75 or (resid 76 and (name N or name CA or name \ C or name O or name CB )) or resid 77 through 105 or (resid 106 and (name N or n \ ame CA or name C or name O or name CB )) or resid 107 through 108 or (resid 109 \ through 116 and (name N or name CA or name C or name O or name CB )) or resid 11 \ 7 through 218 or (resid 219 through 223 and (name N or name CA or name C or name \ O or name CB )) or resid 224 through 233 or (resid 234 and (name N or name CA o \ r name C or name O or name CB )) or resid 235 through 256 or (resid 257 and (nam \ e N or name CA or name C or name O or name CB )) or resid 258 through 262 or (re \ sid 263 and (name N or name CA or name C or name O or name CB )) or resid 264 th \ rough 301 or (resid 302 and (name N or name CA or name C or name O or name CB )) \ or resid 303 through 333 or (resid 334 and (name N or name CA or name C or name \ O or name CB )) or resid 335 through 361)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 16.420 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 48.540 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 29.820 Find NCS groups from input model: 0.500 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 99.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7394 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.063 7880 Z= 0.487 Angle : 0.839 12.378 10766 Z= 0.508 Chirality : 0.052 0.328 1316 Planarity : 0.005 0.090 1396 Dihedral : 16.972 84.942 2568 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 1.06 % Allowed : 10.31 % Favored : 88.63 % Rotamer: Outliers : 1.47 % Allowed : 27.36 % Favored : 71.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.11 (0.25), residues: 1135 helix: 0.58 (0.21), residues: 637 sheet: -2.27 (0.51), residues: 68 loop : -2.53 (0.28), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP D 345 HIS 0.006 0.001 HIS A 195 PHE 0.018 0.002 PHE B 23 TYR 0.008 0.002 TYR C 68 ARG 0.004 0.001 ARG C 233 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2270 Ramachandran restraints generated. 1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2270 Ramachandran restraints generated. 1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 132 time to evaluate : 0.833 Fit side-chains REVERT: A 71 ASN cc_start: 0.8114 (m-40) cc_final: 0.7825 (t0) REVERT: C 224 LEU cc_start: 0.6151 (OUTLIER) cc_final: 0.5921 (mt) REVERT: C 306 LEU cc_start: 0.6683 (mt) cc_final: 0.6349 (pp) outliers start: 9 outliers final: 2 residues processed: 138 average time/residue: 0.2967 time to fit residues: 50.5529 Evaluate side-chains 104 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 101 time to evaluate : 0.732 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 107 ASN Chi-restraints excluded: chain C residue 221 PHE Chi-restraints excluded: chain C residue 224 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 93 optimal weight: 1.9990 chunk 84 optimal weight: 20.0000 chunk 46 optimal weight: 0.0060 chunk 28 optimal weight: 0.6980 chunk 56 optimal weight: 7.9990 chunk 44 optimal weight: 0.9990 chunk 87 optimal weight: 4.9990 chunk 33 optimal weight: 0.7980 chunk 52 optimal weight: 30.0000 chunk 64 optimal weight: 0.9980 chunk 100 optimal weight: 8.9990 overall best weight: 0.6998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 107 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7556 moved from start: 0.2466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 7880 Z= 0.355 Angle : 0.711 13.215 10766 Z= 0.360 Chirality : 0.043 0.217 1316 Planarity : 0.005 0.059 1396 Dihedral : 9.485 89.587 1273 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.53 % Allowed : 8.19 % Favored : 91.28 % Rotamer: Outliers : 7.17 % Allowed : 23.29 % Favored : 69.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.64 (0.25), residues: 1135 helix: 1.10 (0.21), residues: 627 sheet: -2.32 (0.53), residues: 77 loop : -2.42 (0.28), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 60 HIS 0.005 0.001 HIS B 214 PHE 0.015 0.002 PHE A 23 TYR 0.023 0.002 TYR C 105 ARG 0.005 0.001 ARG A 53 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2270 Ramachandran restraints generated. 1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2270 Ramachandran restraints generated. 1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 117 time to evaluate : 0.832 Fit side-chains REVERT: A 71 ASN cc_start: 0.8161 (m-40) cc_final: 0.7696 (t0) REVERT: A 84 ILE cc_start: 0.8109 (OUTLIER) cc_final: 0.7866 (mp) REVERT: A 200 ILE cc_start: 0.8546 (pt) cc_final: 0.8241 (pt) REVERT: B 74 VAL cc_start: 0.8204 (OUTLIER) cc_final: 0.7997 (t) REVERT: B 207 MET cc_start: 0.7363 (OUTLIER) cc_final: 0.6747 (tmm) REVERT: C 319 PHE cc_start: 0.6192 (t80) cc_final: 0.5943 (t80) REVERT: D 241 LEU cc_start: 0.7770 (OUTLIER) cc_final: 0.7535 (mp) REVERT: D 268 GLN cc_start: 0.8327 (OUTLIER) cc_final: 0.7382 (tt0) outliers start: 44 outliers final: 20 residues processed: 154 average time/residue: 0.2216 time to fit residues: 44.5170 Evaluate side-chains 128 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 103 time to evaluate : 0.864 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 SER Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 84 ILE Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 165 THR Chi-restraints excluded: chain A residue 169 ASP Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain B residue 81 ILE Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain B residue 200 ILE Chi-restraints excluded: chain B residue 207 MET Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 221 PHE Chi-restraints excluded: chain C residue 261 ARG Chi-restraints excluded: chain C residue 275 ASP Chi-restraints excluded: chain C residue 312 VAL Chi-restraints excluded: chain D residue 104 VAL Chi-restraints excluded: chain D residue 241 LEU Chi-restraints excluded: chain D residue 266 ASN Chi-restraints excluded: chain D residue 268 GLN Chi-restraints excluded: chain D residue 270 LEU Chi-restraints excluded: chain D residue 334 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 56 optimal weight: 30.0000 chunk 31 optimal weight: 0.6980 chunk 83 optimal weight: 5.9990 chunk 68 optimal weight: 0.9990 chunk 27 optimal weight: 0.9990 chunk 100 optimal weight: 10.0000 chunk 109 optimal weight: 9.9990 chunk 89 optimal weight: 0.7980 chunk 34 optimal weight: 0.4980 chunk 81 optimal weight: 0.0070 chunk 99 optimal weight: 1.9990 overall best weight: 0.6000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7572 moved from start: 0.2961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 7880 Z= 0.299 Angle : 0.625 8.290 10766 Z= 0.320 Chirality : 0.042 0.207 1316 Planarity : 0.004 0.049 1396 Dihedral : 9.091 83.930 1269 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.44 % Allowed : 8.11 % Favored : 91.45 % Rotamer: Outliers : 6.51 % Allowed : 23.78 % Favored : 69.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.17 (0.26), residues: 1135 helix: 1.36 (0.21), residues: 629 sheet: -1.44 (0.54), residues: 80 loop : -2.18 (0.29), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP D 345 HIS 0.004 0.001 HIS B 214 PHE 0.019 0.002 PHE C 247 TYR 0.007 0.001 TYR B 205 ARG 0.003 0.000 ARG A 53 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2270 Ramachandran restraints generated. 1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2270 Ramachandran restraints generated. 1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 96 time to evaluate : 0.804 Fit side-chains REVERT: A 84 ILE cc_start: 0.7972 (OUTLIER) cc_final: 0.7753 (mp) REVERT: A 195 HIS cc_start: 0.7970 (OUTLIER) cc_final: 0.7661 (p-80) REVERT: B 207 MET cc_start: 0.7401 (OUTLIER) cc_final: 0.6809 (tmm) REVERT: D 268 GLN cc_start: 0.8291 (OUTLIER) cc_final: 0.7405 (tt0) outliers start: 40 outliers final: 23 residues processed: 131 average time/residue: 0.2159 time to fit residues: 37.2813 Evaluate side-chains 119 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 92 time to evaluate : 0.799 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 SER Chi-restraints excluded: chain A residue 22 THR Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 84 ILE Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 119 SER Chi-restraints excluded: chain A residue 165 THR Chi-restraints excluded: chain A residue 169 ASP Chi-restraints excluded: chain A residue 195 HIS Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain B residue 77 LEU Chi-restraints excluded: chain B residue 81 ILE Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 169 ASP Chi-restraints excluded: chain B residue 200 ILE Chi-restraints excluded: chain B residue 207 MET Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 221 PHE Chi-restraints excluded: chain C residue 275 ASP Chi-restraints excluded: chain C residue 309 SER Chi-restraints excluded: chain C residue 312 VAL Chi-restraints excluded: chain C residue 325 ILE Chi-restraints excluded: chain D residue 268 GLN Chi-restraints excluded: chain D residue 300 LEU Chi-restraints excluded: chain D residue 334 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 75 optimal weight: 3.9990 chunk 52 optimal weight: 3.9990 chunk 11 optimal weight: 0.0980 chunk 48 optimal weight: 30.0000 chunk 67 optimal weight: 7.9990 chunk 101 optimal weight: 9.9990 chunk 107 optimal weight: 10.0000 chunk 96 optimal weight: 5.9990 chunk 28 optimal weight: 0.0870 chunk 89 optimal weight: 2.9990 chunk 60 optimal weight: 2.9990 overall best weight: 2.0364 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 109 ASN ** D 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7711 moved from start: 0.3498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.013 0.095 7880 Z= 0.881 Angle : 0.958 11.924 10766 Z= 0.478 Chirality : 0.056 0.327 1316 Planarity : 0.006 0.053 1396 Dihedral : 9.867 88.210 1269 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.53 % Allowed : 8.99 % Favored : 90.48 % Rotamer: Outliers : 9.28 % Allowed : 22.31 % Favored : 68.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.92 (0.25), residues: 1135 helix: 0.68 (0.21), residues: 640 sheet: -1.47 (0.58), residues: 62 loop : -2.51 (0.28), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.004 TRP D 345 HIS 0.009 0.003 HIS B 214 PHE 0.028 0.003 PHE C 247 TYR 0.013 0.002 TYR B 205 ARG 0.006 0.001 ARG B 206 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2270 Ramachandran restraints generated. 1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2270 Ramachandran restraints generated. 1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 104 time to evaluate : 0.873 Fit side-chains REVERT: A 83 MET cc_start: 0.7841 (ptt) cc_final: 0.7516 (ttt) REVERT: A 94 ARG cc_start: 0.7440 (mtt180) cc_final: 0.7213 (mtt180) REVERT: A 195 HIS cc_start: 0.8956 (OUTLIER) cc_final: 0.8553 (p-80) REVERT: A 200 ILE cc_start: 0.8711 (OUTLIER) cc_final: 0.8345 (pt) REVERT: A 208 LEU cc_start: 0.8613 (OUTLIER) cc_final: 0.8329 (mt) REVERT: B 74 VAL cc_start: 0.8273 (OUTLIER) cc_final: 0.8036 (t) REVERT: B 203 ARG cc_start: 0.8569 (OUTLIER) cc_final: 0.8215 (mmt90) REVERT: B 207 MET cc_start: 0.7652 (OUTLIER) cc_final: 0.7001 (tmm) REVERT: D 241 LEU cc_start: 0.8021 (OUTLIER) cc_final: 0.7228 (mp) REVERT: D 268 GLN cc_start: 0.8558 (OUTLIER) cc_final: 0.7725 (tt0) outliers start: 57 outliers final: 36 residues processed: 151 average time/residue: 0.2231 time to fit residues: 44.2465 Evaluate side-chains 143 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 99 time to evaluate : 0.908 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 SER Chi-restraints excluded: chain A residue 22 THR Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 110 SER Chi-restraints excluded: chain A residue 119 SER Chi-restraints excluded: chain A residue 123 ASP Chi-restraints excluded: chain A residue 139 SER Chi-restraints excluded: chain A residue 169 ASP Chi-restraints excluded: chain A residue 195 HIS Chi-restraints excluded: chain A residue 200 ILE Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 30 MET Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain B residue 81 ILE Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 114 ILE Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 169 ASP Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain B residue 200 ILE Chi-restraints excluded: chain B residue 203 ARG Chi-restraints excluded: chain B residue 207 MET Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain C residue 93 ILE Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 221 PHE Chi-restraints excluded: chain C residue 270 LEU Chi-restraints excluded: chain C residue 275 ASP Chi-restraints excluded: chain C residue 297 SER Chi-restraints excluded: chain C residue 309 SER Chi-restraints excluded: chain C residue 312 VAL Chi-restraints excluded: chain C residue 315 VAL Chi-restraints excluded: chain C residue 355 HIS Chi-restraints excluded: chain D residue 104 VAL Chi-restraints excluded: chain D residue 241 LEU Chi-restraints excluded: chain D residue 263 ASP Chi-restraints excluded: chain D residue 266 ASN Chi-restraints excluded: chain D residue 268 GLN Chi-restraints excluded: chain D residue 304 LEU Chi-restraints excluded: chain D residue 358 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 1 optimal weight: 0.9990 chunk 79 optimal weight: 0.5980 chunk 44 optimal weight: 0.9980 chunk 91 optimal weight: 0.6980 chunk 74 optimal weight: 0.9980 chunk 0 optimal weight: 0.0970 chunk 54 optimal weight: 30.0000 chunk 96 optimal weight: 10.0000 chunk 27 optimal weight: 0.5980 chunk 36 optimal weight: 1.9990 chunk 21 optimal weight: 0.1980 overall best weight: 0.4378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 266 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7583 moved from start: 0.3550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 7880 Z= 0.255 Angle : 0.602 11.199 10766 Z= 0.310 Chirality : 0.041 0.161 1316 Planarity : 0.004 0.047 1396 Dihedral : 8.787 88.333 1269 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.44 % Allowed : 7.49 % Favored : 92.07 % Rotamer: Outliers : 7.65 % Allowed : 22.80 % Favored : 69.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.15 (0.26), residues: 1135 helix: 1.37 (0.21), residues: 637 sheet: -1.09 (0.61), residues: 62 loop : -2.28 (0.28), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 345 HIS 0.005 0.001 HIS C 358 PHE 0.023 0.001 PHE C 247 TYR 0.004 0.001 TYR B 205 ARG 0.003 0.000 ARG D 262 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2270 Ramachandran restraints generated. 1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2270 Ramachandran restraints generated. 1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 88 time to evaluate : 0.898 Fit side-chains REVERT: A 183 PHE cc_start: 0.8473 (OUTLIER) cc_final: 0.7600 (t80) REVERT: A 195 HIS cc_start: 0.7949 (OUTLIER) cc_final: 0.7686 (p-80) REVERT: A 208 LEU cc_start: 0.8497 (OUTLIER) cc_final: 0.8252 (mt) REVERT: B 207 MET cc_start: 0.7427 (OUTLIER) cc_final: 0.6832 (tmm) REVERT: C 95 LEU cc_start: 0.8780 (OUTLIER) cc_final: 0.8544 (tt) REVERT: D 241 LEU cc_start: 0.7785 (OUTLIER) cc_final: 0.7132 (mp) REVERT: D 268 GLN cc_start: 0.8347 (OUTLIER) cc_final: 0.7565 (tt0) REVERT: D 330 PHE cc_start: 0.4549 (OUTLIER) cc_final: 0.3372 (t80) outliers start: 47 outliers final: 26 residues processed: 129 average time/residue: 0.2189 time to fit residues: 37.2748 Evaluate side-chains 123 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 89 time to evaluate : 0.899 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 SER Chi-restraints excluded: chain A residue 22 THR Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 87 ASP Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 169 ASP Chi-restraints excluded: chain A residue 183 PHE Chi-restraints excluded: chain A residue 195 HIS Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain B residue 81 ILE Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 139 SER Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 169 ASP Chi-restraints excluded: chain B residue 182 GLU Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain B residue 200 ILE Chi-restraints excluded: chain B residue 207 MET Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain C residue 93 ILE Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 221 PHE Chi-restraints excluded: chain C residue 275 ASP Chi-restraints excluded: chain C residue 309 SER Chi-restraints excluded: chain D residue 241 LEU Chi-restraints excluded: chain D residue 265 ILE Chi-restraints excluded: chain D residue 266 ASN Chi-restraints excluded: chain D residue 268 GLN Chi-restraints excluded: chain D residue 304 LEU Chi-restraints excluded: chain D residue 330 PHE Chi-restraints excluded: chain D residue 334 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 62 optimal weight: 0.9980 chunk 26 optimal weight: 0.9980 chunk 107 optimal weight: 7.9990 chunk 89 optimal weight: 2.9990 chunk 49 optimal weight: 30.0000 chunk 8 optimal weight: 0.8980 chunk 35 optimal weight: 0.7980 chunk 56 optimal weight: 50.0000 chunk 103 optimal weight: 0.9990 chunk 12 optimal weight: 0.9980 chunk 61 optimal weight: 1.9990 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 184 ASN ** B 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7639 moved from start: 0.3710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 7880 Z= 0.437 Angle : 0.699 9.942 10766 Z= 0.352 Chirality : 0.045 0.214 1316 Planarity : 0.004 0.048 1396 Dihedral : 9.181 89.253 1269 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.44 % Allowed : 8.37 % Favored : 91.19 % Rotamer: Outliers : 7.33 % Allowed : 24.10 % Favored : 68.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.16 (0.25), residues: 1135 helix: 1.36 (0.21), residues: 633 sheet: -1.22 (0.59), residues: 62 loop : -2.23 (0.28), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP D 345 HIS 0.005 0.002 HIS B 214 PHE 0.019 0.002 PHE C 247 TYR 0.007 0.001 TYR B 205 ARG 0.003 0.001 ARG B 78 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2270 Ramachandran restraints generated. 1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2270 Ramachandran restraints generated. 1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 95 time to evaluate : 0.901 Fit side-chains REVERT: A 90 LEU cc_start: 0.8715 (OUTLIER) cc_final: 0.8492 (pp) REVERT: A 208 LEU cc_start: 0.8565 (OUTLIER) cc_final: 0.8306 (mt) REVERT: B 207 MET cc_start: 0.7486 (OUTLIER) cc_final: 0.6885 (tmm) REVERT: C 269 LYS cc_start: 0.8506 (OUTLIER) cc_final: 0.8175 (tttp) REVERT: D 268 GLN cc_start: 0.8382 (OUTLIER) cc_final: 0.7578 (tt0) REVERT: D 330 PHE cc_start: 0.4583 (OUTLIER) cc_final: 0.3377 (t80) outliers start: 45 outliers final: 30 residues processed: 130 average time/residue: 0.2238 time to fit residues: 38.2221 Evaluate side-chains 130 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 94 time to evaluate : 0.794 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 SER Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 22 THR Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 110 SER Chi-restraints excluded: chain A residue 165 THR Chi-restraints excluded: chain A residue 169 ASP Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain B residue 81 ILE Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 139 SER Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 169 ASP Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain B residue 196 ASP Chi-restraints excluded: chain B residue 200 ILE Chi-restraints excluded: chain B residue 207 MET Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain C residue 93 ILE Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 221 PHE Chi-restraints excluded: chain C residue 269 LYS Chi-restraints excluded: chain C residue 270 LEU Chi-restraints excluded: chain C residue 275 ASP Chi-restraints excluded: chain C residue 309 SER Chi-restraints excluded: chain D residue 237 MET Chi-restraints excluded: chain D residue 266 ASN Chi-restraints excluded: chain D residue 268 GLN Chi-restraints excluded: chain D residue 300 LEU Chi-restraints excluded: chain D residue 304 LEU Chi-restraints excluded: chain D residue 330 PHE Chi-restraints excluded: chain D residue 334 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 78 optimal weight: 20.0000 chunk 60 optimal weight: 1.9990 chunk 90 optimal weight: 0.9980 chunk 59 optimal weight: 1.9990 chunk 106 optimal weight: 0.3980 chunk 66 optimal weight: 1.9990 chunk 65 optimal weight: 0.9980 chunk 49 optimal weight: 20.0000 chunk 42 optimal weight: 0.8980 chunk 63 optimal weight: 0.9980 chunk 32 optimal weight: 0.5980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 216 HIS D 266 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7622 moved from start: 0.3892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 7880 Z= 0.369 Angle : 0.665 10.465 10766 Z= 0.336 Chirality : 0.043 0.202 1316 Planarity : 0.004 0.048 1396 Dihedral : 8.990 88.874 1269 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.44 % Allowed : 8.11 % Favored : 91.45 % Rotamer: Outliers : 7.49 % Allowed : 24.27 % Favored : 68.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.05 (0.26), residues: 1135 helix: 1.48 (0.21), residues: 638 sheet: -1.58 (0.56), residues: 74 loop : -2.20 (0.29), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP D 345 HIS 0.005 0.001 HIS B 214 PHE 0.017 0.002 PHE C 247 TYR 0.005 0.001 TYR B 205 ARG 0.003 0.000 ARG B 78 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2270 Ramachandran restraints generated. 1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2270 Ramachandran restraints generated. 1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 91 time to evaluate : 0.875 Fit side-chains REVERT: A 183 PHE cc_start: 0.8490 (OUTLIER) cc_final: 0.7588 (t80) REVERT: A 208 LEU cc_start: 0.8535 (OUTLIER) cc_final: 0.8275 (mt) REVERT: B 203 ARG cc_start: 0.8552 (OUTLIER) cc_final: 0.8160 (mmt90) REVERT: B 207 MET cc_start: 0.7470 (OUTLIER) cc_final: 0.6856 (tmm) REVERT: C 95 LEU cc_start: 0.8791 (OUTLIER) cc_final: 0.8547 (tt) REVERT: C 269 LYS cc_start: 0.8492 (OUTLIER) cc_final: 0.8168 (tttp) REVERT: D 268 GLN cc_start: 0.8355 (OUTLIER) cc_final: 0.7409 (tt0) REVERT: D 330 PHE cc_start: 0.4510 (OUTLIER) cc_final: 0.3321 (t80) outliers start: 46 outliers final: 32 residues processed: 129 average time/residue: 0.2499 time to fit residues: 42.7813 Evaluate side-chains 131 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 91 time to evaluate : 0.930 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 SER Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 22 THR Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 83 MET Chi-restraints excluded: chain A residue 87 ASP Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 165 THR Chi-restraints excluded: chain A residue 169 ASP Chi-restraints excluded: chain A residue 183 PHE Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain B residue 81 ILE Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 139 SER Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 169 ASP Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain B residue 200 ILE Chi-restraints excluded: chain B residue 203 ARG Chi-restraints excluded: chain B residue 207 MET Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain C residue 93 ILE Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 221 PHE Chi-restraints excluded: chain C residue 269 LYS Chi-restraints excluded: chain C residue 275 ASP Chi-restraints excluded: chain C residue 309 SER Chi-restraints excluded: chain D residue 237 MET Chi-restraints excluded: chain D residue 240 VAL Chi-restraints excluded: chain D residue 265 ILE Chi-restraints excluded: chain D residue 266 ASN Chi-restraints excluded: chain D residue 268 GLN Chi-restraints excluded: chain D residue 300 LEU Chi-restraints excluded: chain D residue 304 LEU Chi-restraints excluded: chain D residue 330 PHE Chi-restraints excluded: chain D residue 334 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 21 optimal weight: 0.9990 chunk 20 optimal weight: 0.5980 chunk 68 optimal weight: 0.8980 chunk 72 optimal weight: 2.9990 chunk 52 optimal weight: 3.9990 chunk 9 optimal weight: 0.0980 chunk 84 optimal weight: 20.0000 chunk 97 optimal weight: 9.9990 chunk 102 optimal weight: 9.9990 chunk 93 optimal weight: 0.7980 chunk 99 optimal weight: 0.6980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 266 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7606 moved from start: 0.3977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 7880 Z= 0.304 Angle : 0.634 11.046 10766 Z= 0.319 Chirality : 0.042 0.220 1316 Planarity : 0.004 0.047 1396 Dihedral : 8.822 88.497 1269 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.44 % Allowed : 7.93 % Favored : 91.63 % Rotamer: Outliers : 7.65 % Allowed : 23.62 % Favored : 68.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.11 (0.26), residues: 1135 helix: 1.58 (0.21), residues: 644 sheet: -1.70 (0.50), residues: 92 loop : -2.08 (0.30), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP D 345 HIS 0.005 0.001 HIS C 358 PHE 0.017 0.001 PHE C 247 TYR 0.005 0.001 TYR B 205 ARG 0.002 0.000 ARG B 78 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2270 Ramachandran restraints generated. 1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2270 Ramachandran restraints generated. 1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 91 time to evaluate : 0.867 Fit side-chains REVERT: A 92 MET cc_start: 0.8716 (mmm) cc_final: 0.8287 (mmt) REVERT: A 183 PHE cc_start: 0.8472 (OUTLIER) cc_final: 0.7581 (t80) REVERT: A 200 ILE cc_start: 0.8575 (OUTLIER) cc_final: 0.8166 (pt) REVERT: B 203 ARG cc_start: 0.8552 (OUTLIER) cc_final: 0.8172 (mmt90) REVERT: B 207 MET cc_start: 0.7451 (OUTLIER) cc_final: 0.6850 (tmm) REVERT: C 95 LEU cc_start: 0.8762 (OUTLIER) cc_final: 0.8537 (tt) REVERT: C 269 LYS cc_start: 0.8493 (OUTLIER) cc_final: 0.8172 (tttp) REVERT: D 268 GLN cc_start: 0.8336 (OUTLIER) cc_final: 0.7464 (tt0) REVERT: D 330 PHE cc_start: 0.4414 (OUTLIER) cc_final: 0.3250 (t80) outliers start: 47 outliers final: 35 residues processed: 131 average time/residue: 0.2292 time to fit residues: 39.0899 Evaluate side-chains 134 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 91 time to evaluate : 0.867 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 SER Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 22 THR Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 87 ASP Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 110 SER Chi-restraints excluded: chain A residue 165 THR Chi-restraints excluded: chain A residue 169 ASP Chi-restraints excluded: chain A residue 183 PHE Chi-restraints excluded: chain A residue 200 ILE Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain B residue 77 LEU Chi-restraints excluded: chain B residue 81 ILE Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 139 SER Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 169 ASP Chi-restraints excluded: chain B residue 182 GLU Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain B residue 195 HIS Chi-restraints excluded: chain B residue 200 ILE Chi-restraints excluded: chain B residue 203 ARG Chi-restraints excluded: chain B residue 207 MET Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain C residue 93 ILE Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 221 PHE Chi-restraints excluded: chain C residue 269 LYS Chi-restraints excluded: chain C residue 275 ASP Chi-restraints excluded: chain C residue 309 SER Chi-restraints excluded: chain C residue 315 VAL Chi-restraints excluded: chain D residue 237 MET Chi-restraints excluded: chain D residue 240 VAL Chi-restraints excluded: chain D residue 265 ILE Chi-restraints excluded: chain D residue 268 GLN Chi-restraints excluded: chain D residue 300 LEU Chi-restraints excluded: chain D residue 304 LEU Chi-restraints excluded: chain D residue 330 PHE Chi-restraints excluded: chain D residue 334 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 102 optimal weight: 9.9990 chunk 60 optimal weight: 0.2980 chunk 43 optimal weight: 0.0470 chunk 78 optimal weight: 20.0000 chunk 30 optimal weight: 0.2980 chunk 90 optimal weight: 0.5980 chunk 94 optimal weight: 2.9990 chunk 99 optimal weight: 0.6980 chunk 65 optimal weight: 1.9990 chunk 105 optimal weight: 0.3980 chunk 64 optimal weight: 0.5980 overall best weight: 0.3278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7546 moved from start: 0.4136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7880 Z= 0.195 Angle : 0.565 10.745 10766 Z= 0.287 Chirality : 0.040 0.228 1316 Planarity : 0.003 0.048 1396 Dihedral : 8.326 85.595 1269 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.35 % Allowed : 6.87 % Favored : 92.78 % Rotamer: Outliers : 5.86 % Allowed : 25.41 % Favored : 68.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.43 (0.26), residues: 1135 helix: 1.90 (0.21), residues: 633 sheet: -1.49 (0.51), residues: 92 loop : -1.98 (0.30), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 345 HIS 0.005 0.001 HIS C 358 PHE 0.019 0.001 PHE C 247 TYR 0.004 0.001 TYR C 102 ARG 0.005 0.000 ARG D 262 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2270 Ramachandran restraints generated. 1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2270 Ramachandran restraints generated. 1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 89 time to evaluate : 0.870 Fit side-chains REVERT: A 92 MET cc_start: 0.8594 (mmm) cc_final: 0.8387 (mmt) REVERT: A 183 PHE cc_start: 0.8463 (OUTLIER) cc_final: 0.7699 (t80) REVERT: A 200 ILE cc_start: 0.8537 (OUTLIER) cc_final: 0.8129 (pt) REVERT: B 207 MET cc_start: 0.7344 (OUTLIER) cc_final: 0.6738 (tmm) REVERT: C 269 LYS cc_start: 0.8477 (OUTLIER) cc_final: 0.8162 (tttp) REVERT: D 268 GLN cc_start: 0.8231 (OUTLIER) cc_final: 0.7450 (tt0) REVERT: D 330 PHE cc_start: 0.4307 (OUTLIER) cc_final: 0.3125 (t80) outliers start: 36 outliers final: 23 residues processed: 118 average time/residue: 0.2446 time to fit residues: 37.7496 Evaluate side-chains 114 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 85 time to evaluate : 0.926 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 SER Chi-restraints excluded: chain A residue 22 THR Chi-restraints excluded: chain A residue 87 ASP Chi-restraints excluded: chain A residue 110 SER Chi-restraints excluded: chain A residue 169 ASP Chi-restraints excluded: chain A residue 183 PHE Chi-restraints excluded: chain A residue 200 ILE Chi-restraints excluded: chain B residue 81 ILE Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 169 ASP Chi-restraints excluded: chain B residue 182 GLU Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain B residue 195 HIS Chi-restraints excluded: chain B residue 200 ILE Chi-restraints excluded: chain B residue 207 MET Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain C residue 93 ILE Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 221 PHE Chi-restraints excluded: chain C residue 269 LYS Chi-restraints excluded: chain C residue 275 ASP Chi-restraints excluded: chain C residue 309 SER Chi-restraints excluded: chain C residue 315 VAL Chi-restraints excluded: chain D residue 237 MET Chi-restraints excluded: chain D residue 268 GLN Chi-restraints excluded: chain D residue 304 LEU Chi-restraints excluded: chain D residue 330 PHE Chi-restraints excluded: chain D residue 334 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 50 optimal weight: 30.0000 chunk 73 optimal weight: 1.9990 chunk 110 optimal weight: 40.0000 chunk 101 optimal weight: 7.9990 chunk 88 optimal weight: 2.9990 chunk 9 optimal weight: 0.3980 chunk 68 optimal weight: 1.9990 chunk 53 optimal weight: 0.0170 chunk 69 optimal weight: 0.9990 chunk 93 optimal weight: 0.9980 chunk 26 optimal weight: 0.0070 overall best weight: 0.4838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7580 moved from start: 0.4222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 7880 Z= 0.254 Angle : 0.602 10.171 10766 Z= 0.302 Chirality : 0.041 0.213 1316 Planarity : 0.003 0.047 1396 Dihedral : 8.556 84.950 1269 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.35 % Allowed : 7.40 % Favored : 92.25 % Rotamer: Outliers : 5.37 % Allowed : 26.06 % Favored : 68.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.46 (0.26), residues: 1135 helix: 1.95 (0.21), residues: 634 sheet: -1.48 (0.50), residues: 92 loop : -1.99 (0.30), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP D 345 HIS 0.005 0.001 HIS C 358 PHE 0.022 0.001 PHE C 247 TYR 0.004 0.001 TYR C 102 ARG 0.002 0.000 ARG A 53 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2270 Ramachandran restraints generated. 1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2270 Ramachandran restraints generated. 1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 91 time to evaluate : 0.891 Fit side-chains REVERT: A 83 MET cc_start: 0.7670 (ptt) cc_final: 0.7296 (ttt) REVERT: A 92 MET cc_start: 0.8634 (mmm) cc_final: 0.8400 (mmt) REVERT: A 183 PHE cc_start: 0.8461 (OUTLIER) cc_final: 0.7629 (t80) REVERT: A 200 ILE cc_start: 0.8551 (OUTLIER) cc_final: 0.8155 (pt) REVERT: B 207 MET cc_start: 0.7386 (OUTLIER) cc_final: 0.6831 (tmm) REVERT: C 269 LYS cc_start: 0.8501 (OUTLIER) cc_final: 0.8194 (tttp) REVERT: D 268 GLN cc_start: 0.8321 (OUTLIER) cc_final: 0.7456 (tt0) REVERT: D 330 PHE cc_start: 0.4344 (OUTLIER) cc_final: 0.3163 (t80) outliers start: 33 outliers final: 25 residues processed: 118 average time/residue: 0.2256 time to fit residues: 34.8962 Evaluate side-chains 121 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 90 time to evaluate : 0.822 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 SER Chi-restraints excluded: chain A residue 22 THR Chi-restraints excluded: chain A residue 87 ASP Chi-restraints excluded: chain A residue 110 SER Chi-restraints excluded: chain A residue 139 SER Chi-restraints excluded: chain A residue 169 ASP Chi-restraints excluded: chain A residue 183 PHE Chi-restraints excluded: chain A residue 200 ILE Chi-restraints excluded: chain B residue 81 ILE Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 139 SER Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 169 ASP Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain B residue 195 HIS Chi-restraints excluded: chain B residue 200 ILE Chi-restraints excluded: chain B residue 207 MET Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain C residue 93 ILE Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 221 PHE Chi-restraints excluded: chain C residue 269 LYS Chi-restraints excluded: chain C residue 275 ASP Chi-restraints excluded: chain C residue 309 SER Chi-restraints excluded: chain C residue 315 VAL Chi-restraints excluded: chain D residue 237 MET Chi-restraints excluded: chain D residue 268 GLN Chi-restraints excluded: chain D residue 300 LEU Chi-restraints excluded: chain D residue 304 LEU Chi-restraints excluded: chain D residue 330 PHE Chi-restraints excluded: chain D residue 334 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 81 optimal weight: 9.9990 chunk 13 optimal weight: 0.6980 chunk 24 optimal weight: 0.9980 chunk 88 optimal weight: 1.9990 chunk 36 optimal weight: 0.3980 chunk 90 optimal weight: 0.5980 chunk 11 optimal weight: 0.0970 chunk 16 optimal weight: 0.8980 chunk 77 optimal weight: 30.0000 chunk 5 optimal weight: 0.8980 chunk 63 optimal weight: 0.5980 overall best weight: 0.4778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4391 r_free = 0.4391 target = 0.207486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.163976 restraints weight = 8616.171| |-----------------------------------------------------------------------------| r_work (start): 0.3944 rms_B_bonded: 1.64 r_work: 0.3516 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3339 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3339 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8237 moved from start: 0.4397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 7880 Z= 0.245 Angle : 0.589 10.376 10766 Z= 0.297 Chirality : 0.040 0.204 1316 Planarity : 0.004 0.047 1396 Dihedral : 8.396 86.175 1269 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.35 % Allowed : 6.78 % Favored : 92.86 % Rotamer: Outliers : 5.86 % Allowed : 25.73 % Favored : 68.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.52 (0.26), residues: 1135 helix: 1.93 (0.21), residues: 643 sheet: -1.46 (0.50), residues: 92 loop : -1.95 (0.30), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 345 HIS 0.005 0.001 HIS C 358 PHE 0.018 0.001 PHE C 247 TYR 0.004 0.001 TYR C 102 ARG 0.003 0.000 ARG B 203 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2417.79 seconds wall clock time: 44 minutes 37.24 seconds (2677.24 seconds total)